The major objective of this Renewal Program Project Application remains as stated in its predecessor, to determine "the molecular basis of regulatory information flow in early embryonic development." However, to a significant extent as a result of our work on this Program, the meaning of these words has been transformed, and this Renewal Application is focused on the opportunity now confronting us to solve the problem of regulatory interaction flow in the embryo by determining the gene regulatory network (GRN) that directs its development. The GRN consists largely of interactions mandated by genomic cis-regulatory sequences controlling genes that encode transcription factors and some signaling components. The initial inputs are maternal factors, and the terminal output in each spatial domain is activation of genes encoding differentiation proteins. In the Davidson Component of the Program, GRN analysis of embryogenesis in the sea urchin, Strongylocentrotus purpuratus will be extended to the whole of the embryo, and almost the whole of embryogenesis (from shortly after fertilization to about 2.5 days). The Fraser Component is focused on novel approaches to imaging the activity of GRNs, using sea urchin and ascidian embryos. In the Levine Component key linkages of the endomesoderm GRN of the sea urchin embryo will be sought in the ascidian embryo, and the possibility will be examined that there is a basal cis-regulatory code for this fundamental process in embryogenesis shared between chordates and echinoderms. The Administrative section will oversee management, budget, and interlaboratory coordination with respect to financial, material and intellectual matters. A Research Core Service Facility similar but not identical to the current one is also requested, the basic role of which is to provide embryos, eggs and nuclear extracts of S. purpuratus to the three Research Components.